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After the scandal caused by killing Pavel Young in a duel, Honor retreats to Grayson until things settle down on Manticore. She intends to oversee the development of her Steading, and overcome the death of Paul Tankersley.

Honor struggles with the survivor's guilt her many battles have left her with, but soon finds that she cannot afford to dwell on her emotions. With the war between Manticore and Haven still raging, the fast-expanding but still inexperienced Grayson Space Navy needs someone to put it in fighting shape. Honor is eventually given the rank of Admiral in the Grayson navy and command of a superdreadnought squadron. She conducts her squadron and the rest of her adoptive nation's fleet through several battle exercises to improve them.

Meanwhile, Haven stages a new operation capturing two planets deep in Alliance territory. A Manticore task force and half the Grayson Navy leave to liberate these planets, but Haven was banking on this and now are sending another task force to destroy Grayson's orbital infrastructure and arm Masada with modern weapons.

The events surrounding her last adventure on Grayson (see The Honor of the Queen) have caused political turmoil on the reactionary planet. Even though she has the support of Protector Benjamin Mayhew IX and the Grayson government and the respect and gratitude of the people of Grayson, several of her fellow Steadholders refuse to accept her and plot to bring down Mayhew's reforms by resorting to terrorism. They sabotage a dome which was being built and financed by Honor. The dome collapses mid-construction and kills dozens of young children. When it appears that the government discovered their conspiracy, they attempt to assassinate Honor but this fails as well. Eventually the conspiracy is revealed to the public and Honor herself, acting in her official capacity as Protector Benjamin's Champion, kills its leader.

Shortly thereafter the Havenite task force arrives to destroy Grayson's orbital infrastructure, but not realizing the size of the Grayson Navy, are defeated by Honor and the ships under her command.

An author's note from David Weber at the end of the book explains Weber's sorrow about the Oklahoma City bombing, which was somewhat similar to the destruction of Williard Mueller Middle School in the story and occurred after the writing of Flag in Exile, but before its publication.[1]